null Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pv4-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:56 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 106 and 0 Target number of residues in the AU: 106 Target solvent content: 0.6581 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 145 Adjusted target solvent content: 0.53 Input MTZ file: 2pv4-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 35.957 47.283 98.695 90.000 90.000 90.000 Input sequence file: 2pv4-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1160 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 49.347 3.600 Wilson plot Bfac: 82.10 2148 reflections ( 99.35 % complete ) and 0 restraints for refining 1278 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3519 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4059 (Rfree = 0.000) for 1278 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.75 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.307 Round 2: 70 peptides, 11 chains. Longest chain 12 peptides. Score 0.443 Round 3: 71 peptides, 10 chains. Longest chain 14 peptides. Score 0.491 Round 4: 76 peptides, 8 chains. Longest chain 19 peptides. Score 0.604 Round 5: 82 peptides, 9 chains. Longest chain 22 peptides. Score 0.613 Taking the results from Round 5 Chains 9, Residues 73, Estimated correctness of the model 19.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2148 reflections ( 99.35 % complete ) and 2196 restraints for refining 995 atoms. 1913 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3845 (Rfree = 0.000) for 995 atoms. Found 6 (6 requested) and removed 31 (3 requested) atoms. Cycle 2: After refmac, R = 0.3742 (Rfree = 0.000) for 935 atoms. Found 3 (6 requested) and removed 12 (3 requested) atoms. Cycle 3: After refmac, R = 0.3547 (Rfree = 0.000) for 899 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 4: After refmac, R = 0.3280 (Rfree = 0.000) for 881 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.3394 (Rfree = 0.000) for 861 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.56 4.38 Search for helices and strands: 0 residues in 0 chains, 932 seeds are put forward Round 1: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.389 Round 2: 67 peptides, 8 chains. Longest chain 17 peptides. Score 0.534 Round 3: 63 peptides, 8 chains. Longest chain 14 peptides. Score 0.501 Round 4: 63 peptides, 8 chains. Longest chain 18 peptides. Score 0.501 Round 5: 62 peptides, 7 chains. Longest chain 14 peptides. Score 0.532 Taking the results from Round 2 Chains 8, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2148 reflections ( 99.35 % complete ) and 1936 restraints for refining 887 atoms. 1708 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3599 (Rfree = 0.000) for 887 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 7: After refmac, R = 0.3299 (Rfree = 0.000) for 872 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 8: After refmac, R = 0.3182 (Rfree = 0.000) for 859 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 9: After refmac, R = 0.3152 (Rfree = 0.000) for 847 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 10: After refmac, R = 0.3125 (Rfree = 0.000) for 841 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.07 3.91 Search for helices and strands: 0 residues in 0 chains, 902 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.325 Round 2: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.405 Round 3: 71 peptides, 11 chains. Longest chain 13 peptides. Score 0.452 Round 4: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.487 Round 5: 68 peptides, 10 chains. Longest chain 14 peptides. Score 0.465 Taking the results from Round 4 Chains 9, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2148 reflections ( 99.35 % complete ) and 1952 restraints for refining 912 atoms. 1733 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3396 (Rfree = 0.000) for 912 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 12: After refmac, R = 0.3526 (Rfree = 0.000) for 885 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 13: After refmac, R = 0.3245 (Rfree = 0.000) for 869 atoms. Found 3 (5 requested) and removed 11 (2 requested) atoms. Cycle 14: After refmac, R = 0.3187 (Rfree = 0.000) for 852 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.3039 (Rfree = 0.000) for 843 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.60 Search for helices and strands: 0 residues in 0 chains, 876 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.293 Round 2: 57 peptides, 10 chains. Longest chain 12 peptides. Score 0.359 Round 3: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.487 Round 4: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.487 Round 5: 60 peptides, 8 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 4 Chains 9, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2148 reflections ( 99.35 % complete ) and 1838 restraints for refining 855 atoms. 1619 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3711 (Rfree = 0.000) for 855 atoms. Found 5 (5 requested) and removed 16 (2 requested) atoms. Cycle 17: After refmac, R = 0.3395 (Rfree = 0.000) for 834 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.3305 (Rfree = 0.000) for 821 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.3156 (Rfree = 0.000) for 813 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.3394 (Rfree = 0.000) for 811 atoms. Found 5 (5 requested) and removed 16 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.93 3.78 Search for helices and strands: 0 residues in 0 chains, 854 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.293 Round 2: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.389 Round 3: 56 peptides, 9 chains. Longest chain 10 peptides. Score 0.393 Round 4: 55 peptides, 8 chains. Longest chain 15 peptides. Score 0.427 Round 5: 55 peptides, 9 chains. Longest chain 14 peptides. Score 0.384 Taking the results from Round 4 Chains 8, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2148 reflections ( 99.35 % complete ) and 1823 restraints for refining 856 atoms. 1643 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3408 (Rfree = 0.000) for 856 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 22: After refmac, R = 0.3552 (Rfree = 0.000) for 844 atoms. Found 3 (5 requested) and removed 6 (2 requested) atoms. Cycle 23: After refmac, R = 0.3368 (Rfree = 0.000) for 827 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 24: After refmac, R = 0.3556 (Rfree = 0.000) for 819 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 25: After refmac, R = 0.3544 (Rfree = 0.000) for 813 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.91 3.76 Search for helices and strands: 0 residues in 0 chains, 854 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 5 peptides. Score 0.230 Round 2: 47 peptides, 8 chains. Longest chain 9 peptides. Score 0.347 Round 3: 50 peptides, 9 chains. Longest chain 7 peptides. Score 0.332 Round 4: 51 peptides, 8 chains. Longest chain 12 peptides. Score 0.388 Round 5: 53 peptides, 10 chains. Longest chain 7 peptides. Score 0.318 Taking the results from Round 4 Chains 8, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2148 reflections ( 99.35 % complete ) and 1827 restraints for refining 851 atoms. 1663 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3727 (Rfree = 0.000) for 851 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 27: After refmac, R = 0.3548 (Rfree = 0.000) for 839 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 28: After refmac, R = 0.3344 (Rfree = 0.000) for 826 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.3150 (Rfree = 0.000) for 822 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2925 (Rfree = 0.000) for 815 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.50 Search for helices and strands: 0 residues in 0 chains, 846 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 6 peptides. Score 0.207 Round 2: 43 peptides, 9 chains. Longest chain 7 peptides. Score 0.253 Round 3: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.274 Round 4: 53 peptides, 10 chains. Longest chain 7 peptides. Score 0.318 Round 5: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.274 Taking the results from Round 4 Chains 10, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2148 reflections ( 99.35 % complete ) and 1661 restraints for refining 798 atoms. 1499 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3494 (Rfree = 0.000) for 798 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 32: After refmac, R = 0.3130 (Rfree = 0.000) for 783 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.3473 (Rfree = 0.000) for 775 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 34: After refmac, R = 0.3204 (Rfree = 0.000) for 768 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.3056 (Rfree = 0.000) for 758 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.61 Search for helices and strands: 0 residues in 0 chains, 786 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.304 Round 2: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.349 Round 3: 57 peptides, 10 chains. Longest chain 11 peptides. Score 0.359 Round 4: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.318 Round 5: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.307 Taking the results from Round 3 Chains 10, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2148 reflections ( 99.35 % complete ) and 1737 restraints for refining 814 atoms. 1559 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3840 (Rfree = 0.000) for 814 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 37: After refmac, R = 0.3553 (Rfree = 0.000) for 810 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 38: After refmac, R = 0.3472 (Rfree = 0.000) for 806 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.3310 (Rfree = 0.000) for 805 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.3230 (Rfree = 0.000) for 805 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.46 4.29 Search for helices and strands: 0 residues in 0 chains, 859 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 5 peptides. Score 0.208 Round 2: 40 peptides, 8 chains. Longest chain 6 peptides. Score 0.268 Round 3: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.256 Round 4: 42 peptides, 8 chains. Longest chain 6 peptides. Score 0.291 Round 5: 45 peptides, 9 chains. Longest chain 7 peptides. Score 0.277 Taking the results from Round 4 Chains 8, Residues 34, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2148 reflections ( 99.35 % complete ) and 1779 restraints for refining 812 atoms. 1651 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3615 (Rfree = 0.000) for 812 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 42: After refmac, R = 0.3539 (Rfree = 0.000) for 800 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 43: After refmac, R = 0.3054 (Rfree = 0.000) for 789 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.3691 (Rfree = 0.000) for 786 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.3106 (Rfree = 0.000) for 785 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.27 4.10 Search for helices and strands: 0 residues in 0 chains, 815 seeds are put forward Round 1: 26 peptides, 6 chains. Longest chain 5 peptides. Score 0.197 Round 2: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.260 Round 3: 33 peptides, 7 chains. Longest chain 6 peptides. Score 0.235 Round 4: 25 peptides, 5 chains. Longest chain 6 peptides. Score 0.243 Round 5: 26 peptides, 5 chains. Longest chain 7 peptides. Score 0.256 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 28, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pv4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2148 reflections ( 99.35 % complete ) and 1354 restraints for refining 690 atoms. 1249 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3630 (Rfree = 0.000) for 690 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3618 (Rfree = 0.000) for 684 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.3408 (Rfree = 0.000) for 679 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.3679 (Rfree = 0.000) for 674 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:00 GMT 2018 Job finished. TimeTaking 22.22 Used memory is bytes: 1514504